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- PDB-1my7: NF-kappaB p65 subunit dimerization domain homodimer N202R mutation -

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Basic information

Entry
Database: PDB / ID: 1my7
TitleNF-kappaB p65 subunit dimerization domain homodimer N202R mutation
ComponentsNF-kappaB p65 (RelA) subunit
KeywordsTRANSCRIPTION / Immunoglobulin / Ig / beta-sandwich / beta-sheet / homodimerDNA-binding / Transcription regulation / Activator / Nuclear protein / Phosphorylation
Function / homology
Function and homology information


SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation ...SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / positive regulation of Schwann cell differentiation / response to cobalamin / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / actinin binding / response to UV-B / non-canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / signal transduction involved in regulation of gene expression / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / response to muramyl dipeptide / positive regulation of vascular endothelial growth factor production / cellular response to angiotensin / general transcription initiation factor binding / response to cAMP / canonical NF-kappaB signal transduction / hair follicle development / neuropeptide signaling pathway / NF-kappaB binding / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / response to muscle stretch / positive regulation of interleukin-12 production / antiviral innate immune response / negative regulation of cytokine production involved in inflammatory response / peptide binding / negative regulation of insulin receptor signaling pathway / response to progesterone / negative regulation of miRNA transcription / negative regulation of angiogenesis / animal organ morphogenesis / response to ischemia / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / protein catabolic process / liver development / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / defense response / response to insulin / negative regulation of protein catabolic process / chromatin DNA binding / positive regulation of interleukin-6 production / cellular response to nicotine / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / histone deacetylase binding / cellular response to hydrogen peroxide / cellular response to tumor necrosis factor / chromatin organization / cellular response to lipopolysaccharide / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / inflammatory response / DNA-binding transcription factor activity
Similarity search - Function
Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. ...Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHuxford, T. / Mishler, D. / Phelps, C.B. / Huang, D.-B. / Sengchanthalangsy, L.L. / Reeves, R. / Hughes, C.A. / Komives, E.A. / Ghosh, G.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/IkappaB alpha complex formation
Authors: Huxford, T. / Mishler, D. / Phelps, C.B. / Huang, D.-B. / Sengchanthalangsy, L.L. / Reeves, R. / Hughes, C.A. / Komives, E.A. / Ghosh, G.
History
DepositionOct 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NF-kappaB p65 (RelA) subunit
B: NF-kappaB p65 (RelA) subunit


Theoretical massNumber of molelcules
Total (without water)26,4902
Polymers26,4902
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-7 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.988, 75.072, 108.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

21B-324-

HOH

31B-391-

HOH

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Components

#1: Protein NF-kappaB p65 (RelA) subunit


Mass: 13244.971 Da / Num. of mol.: 2 / Fragment: residues 191 - 304 (dimerization domain) / Mutation: N202R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RELA / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04207
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.l M sodium HEPES, 0.2 M sodium tartrate, 2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
30.15-0.2 Msodium tartrate1reservoir
41.9-2.1 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: SBC-2 / Detector: CCD / Date: Nov 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→30 Å / Num. all: 39447 / Num. obs: 36240 / % possible obs: 91.8 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 10.2 % / Rsym value: 0.054 / Net I/σ(I): 13.9
Reflection shellResolution: 1.49→1.54 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.327 / % possible all: 82.7
Reflection
*PLUS
Num. measured all: 368554 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 82.7 % / Rmerge(I) obs: 0.327

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1bft

1bft


Resolution: 1.49→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3339 -random
Rwork0.233 ---
all0.247 37805 --
obs0.247 33670 89.1 %-
Refinement stepCycle: LAST / Resolution: 1.49→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 0 271 1944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.43
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.43

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